A thin endocrown restoration was often applied in endodontically treated teeth with vertical bite height loss or inadequate clinical crown length. A model of mandibular molars made by endocrown restoration with 1 mm thickness and 2 mm depth of pulp chamber was constructed and imported into FEA ANSYS v18.0 software. The three CAD/CAM materials, feldspathic (Mark2), lithium disilicate (EMAX), and lava ultimate (LU), were assigned, and the five load indenters were loaded on the full occlusal (FO), occlusal center (OC), central fossa (CF), buccal groove (BG), and mesiobuccal cusp (MC) of restoration in the model. The MinPS and MaxPS of the thin endocrown were significantly higher than those of tooth tissue in five types of loads except for the LU endocrown loaded in the FO group. The smaller the contact surface of the load was, the higher MaxPS and MinPS were. MaxPS and MinPS of the MC were the highest, followed by the BG and CF in the restoration. In the stress distribution of tooth tissue, MaxPS in the LU endocrown accumulated at the external edge of enamel and was significantly higher than MaxPS in Mark2 and EMAX endocrown concentrated on the chamber wall of dentin under OC, CF and BG loads. Within the limitations of this FEA study, the LU endocrown transferred more stress to tooth tissue than Mark2 and EMAX, and the maximum principal stress on endocrown restoration and tooth tissue at the mesiobuccal cusp load was higher than that at the central fossa and buccal groove load.